title: Lipid receptor S1P₁ activation scheme concluded from microsecond all-atom molecular dynamics simulations.
abstract: Sphingosine 1-phosphate (S1P) is a lysophospholipid mediator which activates G protein-coupled sphingosine 1-phosphate receptors and thus evokes a variety of cell and tissue responses including lymphocyte trafficking, endothelial development, integrity, and maturation. We performed five all-atom 700 ns molecular dynamics simulations of the sphingosine 1-phosphate receptor 1 (S1P₁) based on recently released crystal structure of that receptor with an antagonist. We found that the initial movements of amino acid residues occurred in the area of highly conserved W269⁶·⁴⁸ in TM6 which is close to the ligand binding location. Those residues located in the central part of the receptor and adjacent to kinks of TM helices comprise of a transmission switch. Side chains movements of those residues were coupled to the movements of water molecules inside the receptor which helped in the gradual opening of intracellular part of the receptor. The most stable parts of the protein were helices TM1 and TM2, while the largest movement was observed for TM7, possibly due to the short intracellular part starting with a helix kink at P⁷·⁵⁰, which might be the first helix to move at the intracellular side. We show for the first time the detailed view of the concerted action of the transmission switch and Trp (W⁶·⁴⁸) rotamer toggle switch leading to redirection of water molecules flow in the central part of the receptor. That event is a prerequisite for subsequent changes in intracellular part of the receptor involving water influx and opening of the receptor structure.
authors.affiliation: International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland ; Laboratory of Physical Chemistry of Polymers and Membranes, École Polytechnique Fédérale de Lausanne, SB ISIC LCPPM, Lausanne, Switzerland ; Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland.
authors.forename: Shuguang
authors.initials: S
authors.lastname: Yuan
authors.forename: Rongliang
authors.initials: R
authors.lastname: Wu
authors.forename: Dorota
authors.initials: D
authors.lastname: Latek
authors.forename: Bartosz
authors.initials: B
authors.lastname: Trzaskowski
authors.forename: Slawomir
authors.initials: S
authors.lastname: Filipek
mesh_terms: D004252:DNA Mutational Analysis; D008246:Lysophospholipids / Q000737:chemistry / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D049349:Receptors, Lysosphingolipid / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D013110:Sphingosine / Q000031:analogs & derivatives / Q000737:chemistry / Q000378:metabolism; D014867:Water
chemical_list: D008246:Lysophospholipids; D049349:Receptors, Lysosphingolipid; D014867:Water; C060506:sphingosine 1-phosphate; D013110:Sphingosine